Is it reproduce-able on a fresh Kanotix installation (without any Desktop customizations)? I know such problems only from users that customize their desktop look&feel. Do you have a special theme active or something like that? Is it only Skype or affects that other programs too?

I noticed the skype icon was still there but under other transparent stuff and inaccessible.
So I started deleting items from the system tray to get to it.
ended up with some inactive icons, volume, notifications, clock, keyboard, skype etc.
changed some panel setting about overlapping I think and they became active.

kde4 is a little weird sometimes but all in all a good work environment.

Sticking to default look and feel is not an option, I love the retro Kanotix icons/art
and keep all i can but hate the kickoff menu, change all menus to classic
+ folder view on desktop ..

That are exactly such problems I had in mind. Of course nobody forces you to stay with the default look & feel, feel free to customize your desktop as you like. If you share it, some other people could like it as well.

But the point is, that you should be aware that customizations can be the source of such graphical problems. So having the default theme still installed even if you do not use it, is always good for testing purpose.